Both need to be terminated. No matter what. The SE has 1 scsi bus and when using both internal and external drives, both ends should be terminated.
I know you have done a lot of this but here is what I would do.
Take a working file and test it on each one. Do not move the SD card over, use 2 separate ones. I have had 2 of the same brand card where only 1 works with BlueSCSI.
Once you have each device, with its own card, able to boot the machine, name the file hd1.hda on one, and hd2.hda on the other. They must be separate scsi IDs because the SCSI bus on the SE does not differentiate internal/external for IDs. The emulator is using this filename to choose the scsi Id for the HDD it is emulating, so I would expect using the same filename/ID on both BlueSCSIs is all but certain to screw things up.
Now, power wise; I have enough concern running one SD device off termination power, so two I could almost certainly see causing problems. I suggested a HD to floppy power cable for your internal one to supplement 5v and hopefully take load off the bus. Did you ever get the polarity of that correct / working?
Have you checked the 5V level while the PSU is under the load of both devices?
Anything in the log file(s) when the failed attempt at using 2 at once happens?